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Projects

BioFab projects are designed to produce broadly useful collections of standard biological parts that can be made freely available to both academic and commercial users, while also enabling the rapid design and prototyping of genetic constructs needed to support specific needs of partner efforts such as SynBERC Testbeds. The BioFab thus also represents the first significant focused investment in the development of open technology platforms underlying and supporting the next generation of biotechnology. Once fully operational the BioFab facility will be capable of producing tens of thousands of professionally engineered, high quality standard biological parts each year.

C-dog

The Central Dogma (C-dog) project aims to design, build, and characterize a collection of thousands of standard biological parts necessary to control key aspects of genetic expression in a select number of organisms. This parts collection, to be known as the “C. dog.” collection, will support the scaleable rational engineering of the central dogma in E. coli and S. cerevisiae. More specifically, we will design, build, and test a collection of engineered genetic components that control DNA replication, constitutive RNA production, RNA processing and degradation, translation initiation, and protein degradation. For each class of functional genetic element, we will engineer and validate a full suite of specific elements.

The C. dog parts collection will be made available to all academic and commercial researchers. We will release all such parts under the terms of the BioBrick Public Agreements. Doing so will ensure that the BioFab facility will catalyze the formation of an open technology platform supporting the next generation of biotechnology, thereby improving the speed and reducing the costs by which purely academic, translational, and commercial biotechnology research can take place.

SynBERC parts on demand

The BIOFAB is working closely with the Synthetic Biology Engineering Research Center (SynBERC) to develop parts and devices as requested for SynBERC testbed applications. We will make available a standing rapid prototyping service to all SynBERC researchers so that any needed engineered genetic systems can be quickly and effectively designed, assembled, and tested. To realize this goal we will develop over the first project year the following capabilities:

A rapid prototyping request and reporting system, linked to internal SynBERC project reporting systems and the SynBERC intranet, so that an open BioFab project queue so that all SynBERC researchers can request and track BioFab projects.

Integrated design and build capabilities, based on existing open technical standards for defining standardized biological parts and devices combined with best available commercial DNA synthesis capabilities.

SynBERC-commissioned BioFab projects will be made available to the SynBERC researchers, so that they can individually decide based on the best interests of SynBERC, their home institution, and their specific project’s requirements as to if and how to make any BioFab produced materials available to others. We anticipate that some so-engineered BioFab projects will be protected by patent applications initiated by SynBERC researchers and appropriately licensed, while others will be freely shared. Importantly, because the BIOFAB facility will maintain a neutral posture with respect to intellectual property rights, the facility will be able to support many additional partnerships with additional academic and commercial entities, some of whom might hope to work with the BIOFAB in developing both improved open access and propriety parts.This partnership framework might also allow for external organizations to more readily support BIOFAB staff via in kind donations, BIOFAB residencies, and other forms of support.

The BIOFAB -- along with the field of synthetic biology as a whole -- promises significant engineering advances in the design and composition of living systems. It also represents a practical exercise in the capacities and limits of a parts-based approach to biological engineering—organizationally, commercially, and biologically. In this way, the BIOFAB is an ideal testing ground for a range of human practices questions currently in circulation. Many of the security analysts, bioethicists, science studies practitioners and others studying synthetic biology have calibrated their work to the promises and dangers of making biology easier to engineer and making materials and know-how more widely available. To the extent that the BIOFAB successfully achieves its goals it is likely, in short, to ramify across multiple domains. In such a case, as its developers have recognized, the question of how the BIOFAB is organized and orchestrated becomes all the more pressing.

Gaymon Bennett (UC Berkeley) is leading an effort to interface with the BIOFAB in a mode of second-order participation. Specifically, this involves both observing the scientific and organizational practices of the Biofab directors and technicians, as well as contributing that observational analysis as a participating member of the Biofab’s team. Initial work consists of tracking fab development, infrastructure and processes. Ongoing work will involve observing practices of part selection, classification, production and characterization, as well as strategies for soliciting orders, distributing parts, and navigating commercial interests. The work is intended to develop a better understand how work in the BIOFAB is contributing or failing to contribute to the development of synthetic biology today. A central question will be: How is this venue being fashioned and administered given the range of biological, engineering, organizational, and ethical challenges it is likely to confront? Said another way, how are biology, the organization of research, and the ethical practice of science being configured such that the Biofab is an answer to the rethinking and reworking of bioengineering underway today? A goal of Bennett's inquiry is to pose and repose the question of how the BIOFAB is developing in view of such challenges as commercialization and security as work actually unfolds. In examining how synthetic biology as practiced by the BIOFAB is challenging prior configurations of the life-sciences, ethics, and security, the project hopes to illuminate the most effective venues and configurations of practice.

The project builds on three years of work in Human Practices within SynBERC. That mandate, broadly conceived, has been to experiment with an adjusted mode of anthropological inquiry to facilitate the challenge of rethinking and eventually putting into practice, a “post-ELSI” program for synthetic biology. As to the portfolio, a consistent effort of the Berkeley Human Practices lab has been to track the ethical ramifications of research programs and their venues. Such efforts orient inquiry into the problem of designing venues for the intersection of the life sciences, ethics, and security today—a problem which would seem to be a core challenge in the development of the BIOFAB.